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Gene: SNX2 |
Gene summary for SNX2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNX2 | Gene ID | 6643 |
| Gene name | sorting nexin 2 | |
| Gene Alias | TRG-9 | |
| Cytomap | 5q23.2 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O60749 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 6643 | SNX2 | LZE4T | Human | Esophagus | ESCC | 2.21e-14 | 3.32e-01 | 0.0811 |
| 6643 | SNX2 | LZE7T | Human | Esophagus | ESCC | 7.66e-06 | 2.73e-01 | 0.0667 |
| 6643 | SNX2 | LZE8T | Human | Esophagus | ESCC | 5.21e-13 | 4.43e-01 | 0.067 |
| 6643 | SNX2 | LZE24T | Human | Esophagus | ESCC | 8.35e-27 | 8.89e-01 | 0.0596 |
| 6643 | SNX2 | LZE21T | Human | Esophagus | ESCC | 3.09e-03 | 2.02e-01 | 0.0655 |
| 6643 | SNX2 | LZE6T | Human | Esophagus | ESCC | 2.33e-05 | 3.62e-01 | 0.0845 |
| 6643 | SNX2 | P1T-E | Human | Esophagus | ESCC | 1.89e-02 | 3.68e-01 | 0.0875 |
| 6643 | SNX2 | P2T-E | Human | Esophagus | ESCC | 7.36e-53 | 8.67e-01 | 0.1177 |
| 6643 | SNX2 | P4T-E | Human | Esophagus | ESCC | 3.36e-26 | 5.49e-01 | 0.1323 |
| 6643 | SNX2 | P5T-E | Human | Esophagus | ESCC | 1.46e-14 | 3.30e-01 | 0.1327 |
| 6643 | SNX2 | P8T-E | Human | Esophagus | ESCC | 2.35e-33 | 5.80e-01 | 0.0889 |
| 6643 | SNX2 | P9T-E | Human | Esophagus | ESCC | 1.54e-13 | 3.90e-01 | 0.1131 |
| 6643 | SNX2 | P10T-E | Human | Esophagus | ESCC | 1.18e-41 | 6.06e-01 | 0.116 |
| 6643 | SNX2 | P11T-E | Human | Esophagus | ESCC | 4.26e-16 | 5.10e-01 | 0.1426 |
| 6643 | SNX2 | P12T-E | Human | Esophagus | ESCC | 3.13e-41 | 8.88e-01 | 0.1122 |
| 6643 | SNX2 | P15T-E | Human | Esophagus | ESCC | 3.66e-37 | 9.18e-01 | 0.1149 |
| 6643 | SNX2 | P16T-E | Human | Esophagus | ESCC | 7.31e-27 | 5.60e-01 | 0.1153 |
| 6643 | SNX2 | P17T-E | Human | Esophagus | ESCC | 4.79e-05 | 4.18e-01 | 0.1278 |
| 6643 | SNX2 | P19T-E | Human | Esophagus | ESCC | 1.37e-10 | 8.39e-01 | 0.1662 |
| 6643 | SNX2 | P20T-E | Human | Esophagus | ESCC | 6.34e-36 | 9.40e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:001619715 | Esophagus | ESCC | endosomal transport | 168/8552 | 230/18723 | 2.28e-17 | 1.93e-15 | 168 |
| GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
| GO:001648210 | Esophagus | ESCC | cytosolic transport | 124/8552 | 168/18723 | 9.69e-14 | 4.69e-12 | 124 |
| GO:009887615 | Esophagus | ESCC | vesicle-mediated transport to the plasma membrane | 99/8552 | 136/18723 | 1.13e-10 | 3.39e-09 | 99 |
| GO:000716320 | Esophagus | ESCC | establishment or maintenance of cell polarity | 143/8552 | 218/18723 | 2.05e-09 | 4.65e-08 | 143 |
| GO:00070419 | Esophagus | ESCC | lysosomal transport | 83/8552 | 114/18723 | 3.52e-09 | 7.41e-08 | 83 |
| GO:003001018 | Esophagus | ESCC | establishment of cell polarity | 96/8552 | 143/18723 | 1.69e-07 | 2.67e-06 | 96 |
| GO:00421477 | Esophagus | ESCC | retrograde transport, endosome to Golgi | 63/8552 | 91/18723 | 4.58e-06 | 4.87e-05 | 63 |
| GO:00324565 | Esophagus | ESCC | endocytic recycling | 51/8552 | 73/18723 | 2.47e-05 | 2.10e-04 | 51 |
| GO:00083333 | Esophagus | ESCC | endosome to lysosome transport | 40/8552 | 55/18723 | 4.27e-05 | 3.42e-04 | 40 |
| GO:00726735 | Esophagus | ESCC | lamellipodium morphogenesis | 14/8552 | 17/18723 | 2.22e-03 | 9.78e-03 | 14 |
| GO:009758116 | Esophagus | ESCC | lamellipodium organization | 53/8552 | 90/18723 | 7.92e-03 | 2.82e-02 | 53 |
| GO:004819311 | Liver | Cirrhotic | Golgi vesicle transport | 153/4634 | 296/18723 | 1.02e-23 | 6.43e-21 | 153 |
| GO:001648211 | Liver | Cirrhotic | cytosolic transport | 74/4634 | 168/18723 | 3.34e-08 | 1.12e-06 | 74 |
| GO:001619711 | Liver | Cirrhotic | endosomal transport | 93/4634 | 230/18723 | 1.01e-07 | 2.93e-06 | 93 |
| GO:009758111 | Liver | Cirrhotic | lamellipodium organization | 40/4634 | 90/18723 | 3.48e-05 | 4.26e-04 | 40 |
| GO:004214711 | Liver | Cirrhotic | retrograde transport, endosome to Golgi | 34/4634 | 91/18723 | 5.01e-03 | 2.60e-02 | 34 |
| GO:004819321 | Liver | HCC | Golgi vesicle transport | 217/7958 | 296/18723 | 2.58e-27 | 1.02e-24 | 217 |
| GO:001619721 | Liver | HCC | endosomal transport | 154/7958 | 230/18723 | 4.74e-14 | 2.95e-12 | 154 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0414412 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| hsa0414413 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| hsa0414422 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
| hsa0414432 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
| hsa0414427 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
| hsa04144112 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| SNX2 | SNV | Missense_Mutation | novel | c.440N>T | p.Ser147Leu | p.S147L | O60749 | protein_coding | deleterious(0.02) | benign(0.243) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| SNX2 | SNV | Missense_Mutation | c.1114G>C | p.Glu372Gln | p.E372Q | O60749 | protein_coding | deleterious(0) | benign(0.392) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| SNX2 | SNV | Missense_Mutation | c.971N>C | p.His324Pro | p.H324P | O60749 | protein_coding | deleterious(0) | possibly_damaging(0.88) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| SNX2 | SNV | Missense_Mutation | novel | c.1111G>A | p.Glu371Lys | p.E371K | O60749 | protein_coding | deleterious(0.01) | benign(0.324) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SNX2 | SNV | Missense_Mutation | c.354G>A | p.Met118Ile | p.M118I | O60749 | protein_coding | tolerated(0.55) | benign(0) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| SNX2 | SNV | Missense_Mutation | novel | c.857N>C | p.Asn286Thr | p.N286T | O60749 | protein_coding | tolerated(0.06) | benign(0.223) | TCGA-AA-3688-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| SNX2 | SNV | Missense_Mutation | rs138514194 | c.364N>A | p.Val122Met | p.V122M | O60749 | protein_coding | tolerated(0.11) | possibly_damaging(0.631) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| SNX2 | SNV | Missense_Mutation | c.633N>T | p.Lys211Asn | p.K211N | O60749 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| SNX2 | SNV | Missense_Mutation | rs760493667 | c.1465G>A | p.Val489Ile | p.V489I | O60749 | protein_coding | tolerated(0.46) | benign(0.001) | TCGA-AA-A02H-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| SNX2 | SNV | Missense_Mutation | c.240N>T | p.Glu80Asp | p.E80D | O60749 | protein_coding | tolerated(0.13) | possibly_damaging(0.887) | TCGA-AZ-6608-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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